Thesis
The regulatory underpinnings of seasonal run-time variation in Chinook salmon, Oncorhynchus tshawytscha
Washington State University
Master of Science (MS), Washington State University
2023
DOI:
https://doi.org/10.7273/000006388
Abstract
Pacific salmon are an ecologically, economically, and culturally valuable clade of fish that are well-known for their long migrations from the ocean to their freshwater spawning grounds. Unlike other Pacific salmon species, Chinook salmon (Oncorrhynchus tshawytscha) display substantial variation in the time at which they begin their migration, resulting in seasonal run-types known as fall- and spring-run salmon. Seasonal run-time has been found to be highly correlated with SNPs in a ~140 kilobase gene region containing two protein-coding genes: greb1l and rock1. Several co-inherited single nucleotide polymorphisms (SNPs) exist in protein-coding and regulatory regions of greb1l and rock1, making it unclear if run-time variation results from protein structural variation, regulatory evolution, or both. The expression profiles of these genes remain unexplored in Chinook salmon. Regulatory elements – such as enhancers – in the greb1l / rock1 gene region also remain unidentified. The present study aims to elucidate the biological mechanisms by which the greb1l/rock1 gene region controls seasonal run-time by exploring causative SNPs, enhancer regions, and expression of greb1l and rock1 in Chinook salmon. Through the use of RT-PCR, we surveyed expression of greb1l and rock1 across tissue, life stage, run-type, and ohnolog in Chinook salmon. Differential expression of greb1l within brain tissue of fall- and spring-run salmon indicate that greb1l may regulate physiological processes in the hypothalamic-hypophysial region of the brain that control run-time. We also identify evolutionarily conserved enhancer motifs in the greb1l/rock1 gene region and their target genes that may play a role in mediating run-time. The results from our study provide the first expression profile of the greb1l and rock1 and link hypothesized genomic and physiological triggers of run-time in Chinook salmon.
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Details
- Title
- The regulatory underpinnings of seasonal run-time variation in Chinook salmon, Oncorhynchus tshawytscha
- Creators
- Tait Algayer
- Contributors
- Michael P Phelps (Advisor)Joanna L Kelley (Committee Member)Wesley Dowd (Committee Member)Seth Rudman (Committee Member)
- Awarding Institution
- Washington State University
- Academic Unit
- School of Biological Sciences
- Theses and Dissertations
- Master of Science (MS), Washington State University
- Publisher
- Washington State University
- Number of pages
- 78
- Identifiers
- 99901087839901842
- Language
- English
- Resource Type
- Thesis